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The Best Management Practices Statistical Estimator (BMPSE) was developed by the U.S. Geological Survey (USGS), in cooperation with the Federal Highway Administration (FHWA) Office of Project Delivery and Environmental Review to provide planning-level information about the performance of structural best management practices for decision makers, planners, and highway engineers to assess and mitigate possible adverse effects of highway and urban runoff on the Nation's receiving waters (Granato 2013, 2014; Granato and others, 2021a,b). The BMPSE was used to calculate statistics and create input files for fitting the trapezoidal distribution to data from studies documenting the performance of individual structural stormwater...
Categories: Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Best Management Practice (BMP),
Ecology,
Environmental Health,
Event Mean Concentration,
Federal Highway Administration,
This R code (PrepData.R) is used to process the quality controlled legacy nest card data (1985 - 2019) together with the observer names data to produce a capture history data set plot searched twice in 1995 to 1999. Second searches of plot are defined by the PLOTTYPE = “R2” in the nest cards data. Matches are define by the PREVIOUSOBS and PREVIOUSNEST field in the nest card data set but a large number of quality control issue arise in this process and are resolve as detailed in this code. This code produces a data file “chdata.csv” that defines the capture history for each nest and is used as input to Program MARK and JAGS for model fitting and detection estimation. Basic operations include reconciling species and...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
This code produces the memo document and the tabular data files associated with the annual reporting memo.
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
BIOLOGICAL CLASSIFICATION,
This code was created to run a bioenergetics-based model of movement for Galapagos tortoises. It calculates energetic surplus or deficit at a daily time scale based on inputted temperature (6 times a day) and NDVI value (a single value per days), as well as the mass of an individual. It then uses dynamic programming to determine the optimal timing of movement between two foraging habitats, given time-series of NDVI in each habitat, and temperatures in both habitats and in a transition zone between habitats. The model relies on a variety of empirically derived relationships, including allometric relationships, derived for different groups of organisms (i.e., some relationships are based on analyses across multiples...
Categories: Software;
Types: Citation;
Tags: Bioenergetics-based model,
Daily time scale,
Dynamic programming,
Ecuador,
Energetic deficit,
R and Fortran code used in quantitative fatty acid signature analysis (QFASA) robustness to assumption violations.
Categories: Software
This R code (YKDsalinity_QC.R) is used to process the raw legacy salinity data for fixed and random plots (2006 - 2019) and produce the quality controlled legacy salinity data for analysis and sharing (YKDsalinity_QC.csv). Basic operations include transforming missing value to a common code, transforming other variables to match the data dictionary, and cleaning spatial location issues. Of special note is that this QC process discover significant error in location data due to a variety of reasons so the random plot centers are added to the data table and should be used for analysis. The code requires the raw data (“Official_YKD.SALINITY.DATA.MASTER.2020.csv”), a definition of the nest plot study area (“NestPlotStudyAreaBoundary.geojson”),...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: BIOSPHERE,
DATA INTEROPERABILITY,
DATA MANAGEMENT/DATA HANDLING,
DATA REFORMATTING,
EARTH SCIENCE,
The Landscape Simulator is a web-based state-and-transition modelling framework powered by ST-Sim. It is designed to simulate the future vegetation composition of a selected area based on a set of initial conditions, probabilistic transitions, and management actions. This allows land managers to create scenarios for climate adaptation and management.
Categories: Software;
Tags: SageDAT-tool
Protected Lands are the cornerstone around which local, regional and landscape conservation strategies are developed. These lands are designated to preserve functioning natural ecosystems and act as refuges for species. Additionally, protected lands provide public access to recreation and preservation of natural historic sites. In the face of a changing climate, how will these lands be impacted? The Landscape Climate Dashboard allows you to explore future climate projections and soil site sensitivity for federally held protected lands across the California, Pacific Northwest, Great Basin and Great Northern Landscape Conservation Cooperative (LCC) boundaries.
This web map application for the NRCS-funded Sage Grouse Initiative visualizes, distributes, and interactively analyzes spatial data produced by the SGI’s science team. We have provided descriptions and instructions below for how to use and download this sagebrush-steppe data.
Categories: Software;
Tags: SageDAT-tool
The Stochastic Empirical Loading and Dilution Model (SELDM) was developed by the U.S. Geological Survey (USGS), in cooperation with the Federal Highway Administration (FHWA) Office of Project Delivery and Environmental Review to transform complex scientific data into meaningful information about the risk of adverse effects of runoff on receiving waters, the potential need for mitigation measures, and the potential effectiveness of such management measures for reducing these risks (Granato 2013; Granato and Jones, 2014). SELDM is a stochastic model because it uses Monte Carlo methods to produce the random combinations of input variable values needed to generate the stochastic population of values for each component...
Categories: Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: Best Management Practice (BMP),
Event Mean Concentration,
Federal Highway Administration,
Highway-Runoff Database,
Hydrology,
Agent-based models (ABMs) and state-and-transition simulation models (STSMs) have proven useful for understanding processes underlying social-ecological systems and evaluating practical questions about how systems might respond to different scenarios. ABMs can simulate a variety of agents (i.e., autonomous units, such as wildlife, people, or viruses); agent characteristics, decision-making, adaptive behavior, and mobility; and interactions between agents and their environment. STSMs are flexible and intuitive stochastic models of landscape dynamics that can track scenarios and landscape attributes, and integrate diverse data types. Both can be run spatially and track metrics of management success. Due to the complementarity...
Categories: Software;
Tags: Badlands National Park,
USGS Science Data Catalog (SDC),
Wildlife Biology,
analytical modeling,
biota,
The SeaDuckDetectoR is software designed to identify sea ducks and other avian species in aerial photographs. The program is run through R and RStudio. The product includes a .zip file “SeaDuckDetectoR.0.1.0.zip” with the files for installation, and a manual “SeaDuckDetectoR_Manual.docx” explaining how to run the program.
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
BIOLOGICAL CLASSIFICATION,
BIRDS,
EARTH SCIENCE,
Science Keywords,
R code that takes in the nest capture history data (chdata.csv), reformats it for model fitting in Program Mark via the R package RMark. A series of models of increasing complexity are fit and compared using AIC. Output is written to text files for each model but is generally not used or saved. Code can be run to generate model results and R workspaces/ object to inspect parameter estimates. The primary purpose of this code is to explore model structures for predicting detection and as an attempt to reproduce historically used parameter estimates in past nest plot reports (e.g., Fischer et al. 2017 and earlier). Results from ‘Model 7’ are most similar to detection estimates used in the past.
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
R code that takes in the nest capture history data (chdata.csv), reformats it for model fitting in the Bayesian MCMC software JAGS via the R package jagsUI. Various generalized linear mixed models are fit using a Huggins two occasion capture history model structure as in Program Mark. A series of models of increasing complexity are fit and compared using DIC. Model text is written to text files for each model but is generally not used or saved. Posteriors are saved as Rworkspaces or written to text files for use in population estimation (nostpop.R). Code can be run to generate model results and R workspaces/objects to inspect parameter estimates. The primary purpose of this code is to compare various mixed model...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
Originally created by Brad Shults, the GitHub repository was created for markdown code used to quality control survey data and create annual survey reports beginning in 2016. The repository can be found on GitHub (‘https://github.com/bsshults/Teshekpuk-Lake-Molt’). A copy of the master branch that was last committed by user “bsshults” (Brad Shults) on 2/24/20 was downloaded by Maggie Harings on 6/29/21 and stored on the Alaska Regional Data Repository (‘GitHub_Annual_Report_Code’). General file naming structure for repository files is: ‘TMGSurvey_Master_[surveyYear]’ Files ending in the file extension ‘.Rmd’ are used to conduct some quality control and data tidying for original survey data. These files contain comments...
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ALPINE/TUNDRA,
ANIMALS/VERTEBRATES,
ARCTIC TUNDRA,
BIOLOGICAL CLASSIFICATION,
BIOLOGICAL RECORDS,
This R code (eggs.R) inputs the quality controlled nest card data and (1) performs additional quality control on the egg code data, (2) reformat the eggs data into a tidy file of egg observations, (3) summarizes egg data into yearly means of initiation and hatch date based on incubation model, and (4) writes csv files for tidy egg data (eggs.csv) and yearly nest stats (yearstats.csv).
Categories: Data,
Software;
Types: Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
ANIMALS/VERTEBRATES,
The Western Association of Fish and Wildlife Agencies CHAT is intended to provide coarse-scale, non-regulatory wildlife information to support project pre-planning. Users of this interactive map are encouraged to also visit state-specific CHAT sites for more detail and to remember that no online tool is a substitute for on-the-ground surveys and consultation with state wildlife experts. The Western Association of Fish and Wildlife Agencies CHAT was created by state wildlife agencies across the West, using a common framework to define "Crucial Habitat" using a suite of priority datasets. The metadata pages describe how each state compiled their Crucial Habitat data and how the regional data was aggregated.
The ViTexOCR script presents a new method for extracting navigation data from videos with text overlays using optical character recognition (OCR) software. Over the past few decades, it was common for videos recorded during surveys to be overlaid with real-time geographic positioning satellite chyrons including latitude, longitude, date and time, as well as other ancillary data (such as speed, heading, or user input identifying fields). Embedding these data into videos provides them with utility and accuracy, but using the location data for other purposes, such as analysis in a geographic information system, is not possible when only available on the video display. Extracting the text data from imagery using software...
Categories: Software;
Types: Citation,
Downloadable;
Tags: CMGP,
Coastal and Marine Geology Program,
PCMSC,
Pacific Coastal and Marine Science Center,
Remote Sensing,
Topock Marsh is a large wetland adjacent to the Colorado River and main feature of Havasu National Wildlife Refuge (Havasu NWR) in southern Arizona. In 2010, U.S. Fish and Wildlife Service (FWS) and Bureau of Reclamation began a project to improve water management capabilities at Topock Marsh and protect habitats and species. Initial construction required a drawdown, which caused below-average inflows and water depths in 2010-2011. Co-applicants Daniels and Haegele of FORT monitored Topock Marsh during the drawdown and immediately after, thus obtained information on immediate effects. However, stress from the drawdown may have a delayed effect on aquatic resources; additionally, significant changes to the infrastructure...
Categories: Data,
Software;
Types: ArcGIS REST Map Service,
ArcGIS Service Definition,
Downloadable,
Map Service,
OGC WFS Layer,
OGC WMS Layer,
OGC WMS Service;
Tags: 2013,
AZ-04,
Applications and Tools,
Arizona,
CA-08,
The Seedlot Selection Tool (SST) is a web-based mapping application designed to help natural resource managers match seedlots with planting sites based on climatic information. The SST can be used to map current climates or future climates based on selected climate change scenarios. It is tailored for matching seedlots and planting sites, but can be used by anyone interested in mapping climates defined by temperature and water availability. The SST is most valuable as a planning and educational tool because of the uncertainty associated with climate interpolation models and climate change projections. The SST allows the user to control many input parameters, and can be customized for the management practices, climate...
Categories: Software;
Tags: SageDAT-tool
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